Non working time is only implemented in real time as the day progresses, or when using the "Standard Day..." button. When you go in and manually edit the clockings on a day, Timesheet will add exactly what you tell it to. I found that trying to include non-working time while editing was more of a hindrance than a help.
Try setting your start date one day earlier. Everywhere in the program, flexi balances are given at the end of the day. Therefore if you say you want the start balance to be +10 on Tuesday you are saying you want the balance to be +10 on Tuesday at 11:59:59PM. If you then work 4 hours extra on Tuesday, it does not change the fact that Tuesday 11:59:59PM is +10, instead it means Monday 11:59:59PM is +6.
Check the date to are trying to delete records up to. The default is one year before current date. Unless you have been using Timesheet for a year already this will do absolutely nothing. Click on the date to change it.
Sort of. If you go to "General..." on the "Options" menu and check "Clock through midnight", it will let you continue working through midnight rather than complain if you have not already clocked off. Effectively it automatically clocks you out at 11.59pm, and then clocks you back in at 12.00am the day after. However all the reporting of total hours worked will still be done based on calendar dates, and IN/OUT on the main screen will still show first clock in (0.00) and last clock out (11.59pm). The capability is intended primarily for people who mainly work days but occasionally stay after midnight.